I guess as the Deeper well was something only learned about once fred became ill, it was not part of standard Watcher briefing, it took Eve to point Wesley to the books he did not realise he had access to.

I always got the impression that the Council had a vested interest in training their Watchers to see things in 'black and white' so that the Slayer was not distracted by the very real grey areas of human/demon interaction. For that reason I think sometimes Watchers gave a simplified version of events, especially to their teenage girl charges.

That's my interpretation of Joss's famous lack of concern where continuity is involved lol.